The dawn of a decisive battle nears in Leyte Gulf against the Abyssal Fleet, the mysterious enemies that occupy the sea. As the only ones capable of fighting them, Kanmusu—young girls possessing the souls of warships—reorganize in preparation. The Shiratsuyu-class destroyer Shigure is assigned to the First Striking Force, Third Section—also known as 1YB3H.

Unfortunately for Shigure, 1YB3H consists of the remaining few Kanmusu and serves as a diversionary fleet. Needing to confront the Abyssal Fleet head-on, it may well be their first and final mission together. Even so, Shigure refuses to let the enemy take another comrade from her. As they advance toward Leyte Gulf during this suicidal mission, the members of 1YB3H must support each other and persevere to prove their worth as competent ships.

To improve the series' quality, KanColle: Itsuka Ano Umi de was shortened to eight episodes instead of 12.